#'This function is to subset data set based on feature
#'
#'
#' @param Data4Goterm
#' @param ad
#' @param sub_feature
#' @param threshold
#'
#'
#' @return
#' @export
#'
#' @examples
#'
#'
#' Re.Go.adjusted.by.number.junction.2<-GotermAnalysis2GetAllGOTerms_AdjustedByNumOfJunctionWithinOneGene(
#' re.PJ.gene.based,ad="J","J",0.05,"Splice_junction_based")
#'
#' data.pwf2.SJs<-plotPWF2(Re.Go.adjusted.by.number.junction.2[[2]],binsize=30,xlab = "Number of SJs(<binsize> gene bins)")
#'
#' Re.Go.adjusted.by.exon.SJ<-GotermAnalysis2GetAllGOTerms_AdjustedByNumOfJunctionWithinOneGene(
#' re.PJ.gene.based,ad="exon_SJ",sub_feature=NULL,0.05,file_prefix="Exon_Splice_junction_based.xls",gene_model=gene.model)
#'
#'
#'
GotermAnalysis2GetAllGOTerms_AdjustedByNumOfJunctionWithinOneGene<-function(re.gene.based,ad="GL",sub_feature=NULL,threshold,gene_model){
#Data4Goterm<-pData(re.gene.based)
Data4Goterm<-re.gene.based
if(is.null(sub_feature)){Data4Goterm.sub_feature<-Data4Goterm}
else{Data4Goterm.sub_feature<-Data4Goterm[grep(sub_feature,Data4Goterm[,8]),]}
print(dim(Data4Goterm.sub_feature))
Data4Goterm.sub_feature.geneID.NumOfJunctions<-Data4Goterm.sub_feature[,c(1,11)]
print(dim(Data4Goterm.sub_feature.geneID.NumOfJunctions))
Data4Goterm.sub_feature.Sig<-Data4Goterm.sub_feature[which(Data4Goterm.sub_feature[,7]<threshold),]
#GO term analysis using GOSeq
All.gene.id.based.on.sub_feature<-unique(unlist(strsplit(Data4Goterm.sub_feature[,1],"\\+")))
#length(All.gene.id.based.on.sub_feature)
All.gene.id.index<-rep(0,length(All.gene.id.based.on.sub_feature))
names(All.gene.id.index)=All.gene.id.based.on.sub_feature
All.genes.based.on.Sig.sub_feature<-unique(unlist(strsplit(Data4Goterm.sub_feature.Sig[,1],"\\+")))
gene.DE_interest<-as.integer(which( All.gene.id.based.on.sub_feature %in% All.genes.based.on.Sig.sub_feature ))
All.gene.id.index[gene.DE_interest]<-1
print(length(All.gene.id.index))
gene.with.matched.junction<-which(Data4Goterm.sub_feature.geneID.NumOfJunctions[,1] %in% c(names(All.gene.id.index)))
num.junction.4.matched.gene<-Data4Goterm.sub_feature.geneID.NumOfJunctions[gene.with.matched.junction,2]
names.4.matched.gene<-Data4Goterm.sub_feature.geneID.NumOfJunctions[gene.with.matched.junction,1]
All.gene.id.index.2<-All.gene.id.index[which(names(All.gene.id.index) %in% c(names.4.matched.gene))]
print(length(All.gene.id.index.2))
print(All.gene.id.index.2)
if(ad=="GL"){
pwf.DE_interest=nullp(All.gene.id.index.2,"mm10","ensGene",plot.fit = FALSE)
}
else
{
pwf.DE_interest=nullp(All.gene.id.index.2,"mm10","ensGene",bias.data = num.junction.4.matched.gene,plot.fit = FALSE)
}
#GO.wall.DE_interest=goseq2(pwf.DE_interest,"mm10","ensGene",gene.model=gene_model,use_genes_without_cat=TRUE)
GO.wall.DE_interest=goseq2(pwf.DE_interest,"mm10","ensGene",gene.model=gene_model)
enriched.GO.DE_interest=GO.wall.DE_interest[p.adjust(GO.wall.DE_interest$over_represented_pvalue,method="BH")<threshold,]
re<-list()
re[[1]]<-GO.wall.DE_interest
re[[2]]<-pwf.DE_interest
return(re)
}
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